International Journal of Marine Science 2015, Vol.5, No.55: 1-9
2
populations is referred to as genetic population
structure, and in the marine environment it has been
reviewed extensively by (Laikre et al., 2005) and
Waples and Gaggiotti (2006).
Gene flow (gene migration) is the movement o
or
within and between populations. It is
influenced by a number of factors such as natural
selection, genetic drift and mutation, in addition to the
mobility of organisms which tend to increase the
migratory potential; gene flow between two populations
can also result in reducing the genetic variation
between the two groups. Gene flow powerfully acts
against
Slatkin, 1985). Marine species with
planktonic larvae are assumed demographically open,
with recruitment mostly from external sources (Caley
et al., 1996)
A successful aquaculture practice (after careful
selection of the site) must be based on identification of
the cultivable species, which is reported to be so
complex in the case of shrimps owing to its phenotypic
similarity and may be impossible in the absence of
external characters (Palumbi and Benzie, 1991;
Baldwin et al., 1998). Mitochondrial DNA (mtDNA)
has been extensively used in PCR-based studies on
food authenticity, population structures, phylogeography
and phylogenetic relationships at different taxonomic
levels (Pascoal et al., 2008).
The application of DNA markers has allowed rapid
progress in aquaculture investigations of genetic
variability and inbreeding, parentage assignments,
species and strain identification, and the construction
of high-resolution genetic linkage maps for aquaculture
species (Jahmori, 2011). For molecular analysis, these
markers are first amplified by PCR using conserved
primers and the amplicons are sequenced. Sequencing
data are then aligned and compared using appropriate
bioinformatics tools. There have been considerable
advances made in recent years, to provoke the ease
and utilization of molecular markers. Such markers
will assist in the development of the penaeid
broodstock selection. One of the most efficient
current methods to determine differentiation between
and within species is by the use of mitochondrial
DNA (mtDNA) and microsatellites (Jahromi, 2011).
Molecular phylogeny of western Atlantic Farfantepenaeus
and Litopenaeus shrimp based on mitochondrial 16S
partial sequences was done by (Maggioni et al.,
2009) .while a molecular phylogeny of the deep-sea
penaeid shrimp genus
Parapenaeus
was studied by
(Chien-Hui et al., 2015) where novel nucleotide
sequence data from five different genes (COI, 16S,
12S, NaK and PEPCK) were collected to estimate
phylogenetic relationships and taxonomic status
amongst all but one subspecies in this genus.
On the other hand and from the commercial point of
view, the black giant tiger shrimp (
P. monodon
) may
be marketed together with the green tiger shrimp (
P.
semisulcatus
) without any specific labeling, although
recent studies have provided evidence of some
divergence between both species (Pascoal et al., 2008).
Also the marketing of
F. indicus
may be complicated
to its anatomical similarities with respect to the
banana shrimp
F. merguiensis
, which is of lower
commercial value. The use of molecular tools is
therefore a suitable strategy to avoid such problems.
In the present study partial 16S rRNA mtDNA gene
was utilised to assess diversity and investigate the
phylogenetic relationships among four shrimp species
namely
Finneropenaeus indicus, Penaeus monodon, P.
semisulcatus
and
Metapenaeus monoceros.
2 Materials and Methods
2.1 Collection site and shrimps used in the study
The collection sites were chosen along the Sudanese
Red Sea coast which extends for 750 km in the eastern
part of Africa. Two well established and easily
accessible aquaculture farms, Alkhairat aquafarm and
Baaboud aquafarm were chosen to represent semi-
intensive and intensive mode of aquaculture respectively.
Wild Mersas (Halaka in the north and Heidub in the
south) and trawling areas represent wild normal
shrimp fishing grounds (Figure 1).
All shrimp samples (Table 1) used in this study were
brought either alive or on ice to the laboratory, sorted
and identified based on morphology according to FAO
(1983) and (Vine) 1986.
2.2 DNA extraction, Amplification and sequencing
Genomic DNA was extracted from 0.2 gm of frozen
muscular tissue using DNeasy Tissue kit (QIAGEN,
Darmstadt, Germany) following the manufacturer’s
description. Extracted genomic DNA was diluted to a
working concentration of 50-100 ng/µl in de-ionized
